AMBER Archive (2005)

Subject: AMBER: no corrected reaction field energy in *.out files after running mm_pbsa

From: haixiao jin (jinhx952_at_gmail.com)
Date: Sun Jun 12 2005 - 21:04:40 CDT

dear amber users,
I make 1mm_pbsa.in to sampling snapshots from a trajectory and make
2mm_pbsa.in to get bind free energy analysis, there are the two files.

1mm_pbsa.in
#sampling snapshots from a trajectory
###############################################################################
@GENERAL
#
PREFIX npt
PATH ./snapshot
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
#
################################################################################
@MAKECRD
BOX YES
NTOTAL 39286
NSTART 500
NSTOP 900
NFREQ 8
#
NUMBER_LIG_GROUPS 1
LSTART 5564
LSTOP 5640
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 5563
#
#################################################################################
@TRAJECTORY
#
TRAJECTORY ./1npt.mdcrd
#
################################################################################
@PROGRAMS
DELPHI /usr/people/yjjiang/program/delphi/delphi/delphi
#

2mm_pbsa.in
#bind free energy analysis
################################################################################
@GENERAL
PREFIX npt
PATH ./snapshot
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./com.prmtop
RECPT ./PKABD8.prmtop
LIGPT ./BD8.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
#
NM 0
#
################################################################################
@DELPHI
#
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2.5
LINIT 3000
BNDCON 4
SALT 0.1
CHARGE ./delphi.crg
SIZE ./delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.92
#
################################################################################@MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 0
RADII ./atmtypenumbers
#
#################################################################################
@PROGRAMS
#
# Program executables and paths
#
DELPHI /usr/people/yjjiang/program/delphi/delphi/delphi
#
################################################################################

I can get the sampling snapshots form a trajectory successfully, but
it ends unmornally while running "nohup mm_pbsa.pl 2mm_pbsa.in >
bind.log &"

I can get sander_com.in, sander_rec.in, sander_lig.in
npt_com.all.out, npt_rec.all.out, npt_lig.all.out, mdinfo, restrt,
npt_statistic.in, npt_statistic.out, and sampling, bind.

In the bind.log:
Reading files:
Reading npt_com.all.out
WARNING: missing SURF for MS in 2 ----taken form 1
WARNING: missing SURF for MS in 4 ----taken form 3
WARNING: missing SURF for MS in 10 ----taken form 9
WARNING: missing SURF for MS in 30 ----taken form 29
WARNING: missing SURF for MS in 42 ----taken form 41
Reading npt_rec.all.out
WARNING: missing SURF for MS in 2 ----taken form 1
WARNING: missing SURF for MS in 4 ----taken form 3
WARNING: missing SURF for MS in 10 ----taken form 9
WARNING: missing SURF for MS in 30 ----taken form 29
WARNING: missing SURF for MS in 42 ----taken form 41
Calc missing parameters
No values for MM_ELE existing ------skipping
No values for MM_GAS existing ------skipping

AND, in npt_rec.all .out, npt_com.all.out npt_lig.all.out, there are
no corrected reaction field energy.

 In npt_lig.all.out, surface area can be calculate form 1 to 51, but
in npt_com.all.out, npt_rec.all.out, the suface area are missing in
3,5,11,31,43, it seems that those missing is related to the WARNING in
bind.log. i have no idea to solve the problem. any suggestion is
appreciated.
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